Human v1.2 - #148
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metabolicTasks_Essential.xls are tasks that are essential for any human cell, whereas metabolicTasks_Full.xls is a more extensive list of tasks that may include some tissue-specific tasks.
No reason to have this metabolite in as part of this media formulation for this metabolic task.
Also remove inactivated reactions prior to export because some software packages confuse these as active reactions.
- These files had been dealt with in #141, now only keep the xlsx version.
- Newly assigned KEGG rxn id to HMR_4284 through manual curation
- adjust and use this function for updating grRules and other related fields - add notes to the model change log files
Major mass-rebalance of HumanGEM
feat: add model annotations prior to exporting SBML
This update is implemented by running script `rebalanceHumanGEM.m`: - 11 rxns are fixed for incorrect reversibility info (#113) - 4 met names are changed by replacing space with hyphen - 6 new mets are added - 21 new transport/exchange rxns are added through expanding existing mets to 20 new comps - 465 unique mets are updated with new formula/charge - 729 rxn equations are updated (not sure the reason) - 203 duplicated rxns are removed - 196 rxns are blocked due to misuse of R group or pool mets - 10 previously inactivated reactions are reopened - 34 duplicated mets are merged - 27 unique mets are modified with updated external identifiers - 16 rxns are modified with updated external identifiers - 38 grRules are retrieved from their duplicated and removed counterparts - modified annotation information is also updated to the `humanGEMRxn/MetAssoc.JSON` files - All modifications are saved to `rebalance_modelChanges_mets/rxns.tsv` for tracking the changes
JonathanRob
approved these changes
Nov 24, 2019
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Main improvements in this PR:
humanGEMRxn/MetAssoc.JSONandrebalance_modelChanges_mets/rxns.tsvfiles